Methamphetamine is a commonly abused central nervous system stimulant. The San Diego County Medical Examiner’s Office has seen increasing positive methamphetamine cases that do not have a suitable blood sample for analysis. We compare liver, vitreous, and central blood levels of methamphetamine and the metabolite amphetamine to levels in peripheral blood samples in 18 medical examiner cases. Specimens were screened by ELISA and confirmed by GCMS analysis following liquid-liquid extraction. Methamphetamine central blood to peripheral blood ratios averaged 1.61 (± 0.48), vitreous to peripheral blood 1.63 (± 0.75) and liver to peripheral blood 5.68 (± 2.32). The data suggests that in cases where blood is not available, vitreous and liver specimens are useful in confirming methamphetamine use.