diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3b1a34c1..077c46fa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@
 * Generate a simplified CDI specification by default. This means that entities in the common edits in a spec are not included in device definitions.
 * Also return an error from the nvcdi.New constructor instead of panicing.
 * Detect XOrg libraries for injection and CDI spec generation.
+* Add `nvidia-container-runtime.modes.cdi.annotation-prefixes` config option that allows the CDI annotation prefixes that are read to be overridden.
 
 * [libnvidia-container] Fix segmentation fault when RPC initialization fails.
 * [libnvidia-container] Build centos variants of the NVIDIA Container Library with static libtirpc v1.3.2.
diff --git a/internal/config/config_test.go b/internal/config/config_test.go
index 4c378d55..72f03336 100644
--- a/internal/config/config_test.go
+++ b/internal/config/config_test.go
@@ -71,7 +71,8 @@ func TestGetConfig(t *testing.T) {
 							MountSpecPath: "/etc/nvidia-container-runtime/host-files-for-container.d",
 						},
 						CDI: cdiModeConfig{
-							DefaultKind: "nvidia.com/gpu",
+							DefaultKind:        "nvidia.com/gpu",
+							AnnotationPrefixes: []string{"cdi.k8s.io/"},
 						},
 					},
 				},
@@ -92,6 +93,7 @@ func TestGetConfig(t *testing.T) {
 				"nvidia-container-runtime.runtimes = [\"/some/runtime\",]",
 				"nvidia-container-runtime.mode = \"not-auto\"",
 				"nvidia-container-runtime.modes.cdi.default-kind = \"example.vendor.com/device\"",
+				"nvidia-container-runtime.modes.cdi.annotation-prefixes = [\"cdi.k8s.io/\", \"example.vendor.com/\",]",
 				"nvidia-container-runtime.modes.csv.mount-spec-path = \"/not/etc/nvidia-container-runtime/host-files-for-container.d\"",
 				"nvidia-ctk.path = \"/foo/bar/nvidia-ctk\"",
 			},
@@ -111,6 +113,10 @@ func TestGetConfig(t *testing.T) {
 						},
 						CDI: cdiModeConfig{
 							DefaultKind: "example.vendor.com/device",
+							AnnotationPrefixes: []string{
+								"cdi.k8s.io/",
+								"example.vendor.com/",
+							},
 						},
 					},
 				},
@@ -134,6 +140,7 @@ func TestGetConfig(t *testing.T) {
 				"mode = \"not-auto\"",
 				"[nvidia-container-runtime.modes.cdi]",
 				"default-kind = \"example.vendor.com/device\"",
+				"annotation-prefixes = [\"cdi.k8s.io/\", \"example.vendor.com/\",]",
 				"[nvidia-container-runtime.modes.csv]",
 				"mount-spec-path = \"/not/etc/nvidia-container-runtime/host-files-for-container.d\"",
 				"[nvidia-ctk]",
@@ -155,6 +162,10 @@ func TestGetConfig(t *testing.T) {
 						},
 						CDI: cdiModeConfig{
 							DefaultKind: "example.vendor.com/device",
+							AnnotationPrefixes: []string{
+								"cdi.k8s.io/",
+								"example.vendor.com/",
+							},
 						},
 					},
 				},
diff --git a/internal/config/runtime.go b/internal/config/runtime.go
index 0248754e..8ff8c6e8 100644
--- a/internal/config/runtime.go
+++ b/internal/config/runtime.go
@@ -19,6 +19,7 @@ package config
 import (
 	"fmt"
 
+	"github.com/container-orchestrated-devices/container-device-interface/pkg/cdi"
 	"github.com/pelletier/go-toml"
 	"github.com/sirupsen/logrus"
 )
@@ -52,6 +53,8 @@ type cdiModeConfig struct {
 	SpecDirs []string `toml:"spec-dirs"`
 	// DefaultKind sets the default kind to be used when constructing fully-qualified CDI device names
 	DefaultKind string `toml:"default-kind"`
+	// AnnotationPrefixes sets the allowed prefixes for CDI annotation-based device injection
+	AnnotationPrefixes []string `toml:"annotation-prefixes"`
 }
 
 type csvModeConfig struct {
@@ -98,6 +101,9 @@ func GetDefaultRuntimeConfig() *RuntimeConfig {
 			},
 			CDI: cdiModeConfig{
 				DefaultKind: "nvidia.com/gpu",
+				AnnotationPrefixes: []string{
+					cdi.AnnotationPrefix,
+				},
 			},
 		},
 	}
diff --git a/internal/modifier/cdi.go b/internal/modifier/cdi.go
index a5f42eb8..879967b9 100644
--- a/internal/modifier/cdi.go
+++ b/internal/modifier/cdi.go
@@ -18,6 +18,7 @@ package modifier
 
 import (
 	"fmt"
+	"strings"
 
 	"github.com/NVIDIA/nvidia-container-toolkit/internal/config"
 	"github.com/NVIDIA/nvidia-container-toolkit/internal/config/image"
@@ -67,7 +68,7 @@ func getDevicesFromSpec(logger *logrus.Logger, ociSpec oci.Spec, cfg *config.Con
 		return nil, fmt.Errorf("failed to load OCI spec: %v", err)
 	}
 
-	_, annotationDevices, err := cdi.ParseAnnotations(rawSpec.Annotations)
+	annotationDevices, err := getAnnotationDevices(cfg.NVIDIAContainerRuntimeConfig.Modes.CDI.AnnotationPrefixes, rawSpec.Annotations)
 	if err != nil {
 		return nil, fmt.Errorf("failed to parse container annotations: %v", err)
 	}
@@ -107,6 +108,38 @@ func getDevicesFromSpec(logger *logrus.Logger, ociSpec oci.Spec, cfg *config.Con
 	return nil, nil
 }
 
+// getAnnotationDevices returns a list of devices specified in the annotations.
+// Keys starting with the specified prefixes are considered and expected to contain a comma-separated list of
+// fully-qualified CDI devices names. If any device name is not fully-quality an error is returned.
+// The list of returned devices is deduplicated.
+func getAnnotationDevices(prefixes []string, annotations map[string]string) ([]string, error) {
+	devicesByKey := make(map[string][]string)
+	for key, value := range annotations {
+		for _, prefix := range prefixes {
+			if strings.HasPrefix(key, prefix) {
+				devicesByKey[key] = strings.Split(value, ",")
+			}
+		}
+	}
+
+	seen := make(map[string]bool)
+	var annotationDevices []string
+	for key, devices := range devicesByKey {
+		for _, device := range devices {
+			if !cdi.IsQualifiedName(device) {
+				return nil, fmt.Errorf("invalid device name %q in annotation %q", device, key)
+			}
+			if seen[device] {
+				continue
+			}
+			annotationDevices = append(annotationDevices, device)
+			seen[device] = true
+		}
+	}
+
+	return annotationDevices, nil
+}
+
 // Modify loads the CDI registry and injects the specified CDI devices into the OCI runtime specification.
 func (m cdiModifier) Modify(spec *specs.Spec) error {
 	registry := cdi.GetRegistry(
diff --git a/internal/modifier/cdi_test.go b/internal/modifier/cdi_test.go
new file mode 100644
index 00000000..88ff697a
--- /dev/null
+++ b/internal/modifier/cdi_test.go
@@ -0,0 +1,92 @@
+/**
+# Copyright (c) NVIDIA CORPORATION.  All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+**/
+
+package modifier
+
+import (
+	"fmt"
+	"testing"
+
+	"github.com/stretchr/testify/require"
+)
+
+func TestGetAnnotationDevices(t *testing.T) {
+	testCases := []struct {
+		description     string
+		prefixes        []string
+		annotations     map[string]string
+		expectedDevices []string
+		expectedError   error
+	}{
+		{
+			description: "no annotations",
+		},
+		{
+			description: "no matching annotations",
+			prefixes:    []string{"not-prefix/"},
+			annotations: map[string]string{
+				"prefix/foo": "example.com/device=bar",
+			},
+		},
+		{
+			description: "single matching annotation",
+			prefixes:    []string{"prefix/"},
+			annotations: map[string]string{
+				"prefix/foo": "example.com/device=bar",
+			},
+			expectedDevices: []string{"example.com/device=bar"},
+		},
+		{
+			description: "multiple matching annotations",
+			prefixes:    []string{"prefix/", "another-prefix/"},
+			annotations: map[string]string{
+				"prefix/foo":         "example.com/device=bar",
+				"another-prefix/bar": "example.com/device=baz",
+			},
+			expectedDevices: []string{"example.com/device=bar", "example.com/device=baz"},
+		},
+		{
+			description: "multiple matching annotations with duplicate devices",
+			prefixes:    []string{"prefix/", "another-prefix/"},
+			annotations: map[string]string{
+				"prefix/foo":         "example.com/device=bar",
+				"another-prefix/bar": "example.com/device=bar",
+			},
+			expectedDevices: []string{"example.com/device=bar"},
+		},
+		{
+			description: "invalid devices",
+			prefixes:    []string{"prefix/"},
+			annotations: map[string]string{
+				"prefix/foo": "example.com/device",
+			},
+			expectedError: fmt.Errorf("invalid device %q", "example.com/device"),
+		},
+	}
+
+	for _, tc := range testCases {
+		t.Run(tc.description, func(t *testing.T) {
+			devices, err := getAnnotationDevices(tc.prefixes, tc.annotations)
+			if tc.expectedError != nil {
+				require.Error(t, err)
+				return
+			}
+
+			require.NoError(t, err)
+			require.ElementsMatch(t, tc.expectedDevices, devices)
+		})
+	}
+}