diff --git a/GPU/Common/ShaderId.cpp b/GPU/Common/ShaderId.cpp
index 9297bc7087..b6183e93d7 100644
--- a/GPU/Common/ShaderId.cpp
+++ b/GPU/Common/ShaderId.cpp
@@ -236,6 +236,12 @@ void ComputeFragmentShaderID(ShaderID *id_out, uint32_t vertType) {
 		}
 
 		id.SetBit(FS_BIT_LMODE, lmode);
+		if (enableAlphaTest) {
+			// 5 bits total.
+			id.SetBit(FS_BIT_ALPHA_TEST);
+			id.SetBits(FS_BIT_ALPHA_TEST_FUNC, 3, gstate.getAlphaTestFunction());
+			id.SetBit(FS_BIT_ALPHA_AGAINST_ZERO, IsAlphaTestAgainstZero());
+		}
 		if (enableColorTest) {
 			// 4 bits total.
 			id.SetBit(FS_BIT_COLOR_TEST);