Organ transplant recipients (OTR) have a substantially elevated risk of squamous cell skin carcinoma (SCSC), largely attributed to immunosuppressive medications used to prevent graft rejection, although data to support the role of newer drugs on SCSC risk are sparse. We investigated the association between immunosuppressive medications and SCSC risk among cardiac and renal transplant recipients in the SCOT cohort study. Incident cases were ascertained through medical record review after self-report of skin biopsy (N=170). Controls without SCSC (N=324) were matched to cases on: gender, age, race, transplant year, hospital, donor type, organ transplanted, and time between transplant and interview. Conditional logistic regression was used to evaluate the association between specific medications and SCSC. Users of the older anti-metabolite azathioprine were more than twice as likely to develop SCSC (OR=2.69; 95%CI 1.23–5.84) compared to non-users. In contrast, the newer anti-metabolite preparations (i.e., mycophenolic acid [MPA]) were associated with lower SCSC risk (OR=0.43; 95%CI 0.27–0.66). This inverse association between MPA and SCSC persisted among OTR with no history of azathioprine use, even after adjustment for simultaneous use of the calcineurin inhibitor tacrolimus (OR=0.50; 95%CI 0.31–0.81). Our data suggest that the increased risk of SCSC historically associated with azathioprine is not seen in OTR prescribed newer regimens, including MPA and tacrolimus.