Background. There was a 6-month shortage of antiretrovirals (cART) in Kenya. Methods. We assessed morbidity, mortality, and loss to follow-up (LTFU) in this retrospective analysis of adults who were enrolled during the six-month period with restricted cART (cap) or the six months prior (pre-cap) and eligible for cART at enrollment by the pre-cap standard. Cox models were used to adjust for potential confounders. Results. 9009 adults were eligible for analysis: 4,714 pre-cap and 4,295 during the cap. Median number of days from enrollment to cART initiation was 42 pre-cap and 56 for the cap (P < 0.001). After adjustment, individuals in the cap were at higher risk of mortality (HR = 1.21; 95% CI : 1.06–1.39) and LTFU (HR = 1.12; 95% CI : 1.04–1.22). There was no difference between the groups in their risk of developing a new AIDS-defining illness (HR = 0.92 95% CI 0.82–1.03). Conclusions. Rationing of cART, even for a relatively short period of six months, led to clinically adverse outcomes.