Primary care providers play an important gatekeeping role in ensuring appropriate referrals to secondary care facilities. This cross-sectional study aimed to determine the level, pattern and rate of referrals from health clinics to hospitals in the public sector, and whether the placement of resident family medicine specialist (FMS) had made a significant difference. The study was carried out between March and April in 2012, involving 28 public primary care clinics. It showed that the average referral rate was 1.56% for clinics with resident FMS and 1.94% for those without resident FMS, but it was not statistically significant. Majority of referred cases were considered appropriate (96.1%). Results of the multivariate analysis showed that no prior consultation with senior healthcare provider and illnesses that were not severe and complex were independently associated with inappropriate referrals. Severity, complexity or uncertain diagnosis of patients' illness or injury significantly contributed to unavoidable referrals. Adequate facilities or having more experienced doctors could have avoided 14.5% of the referrals. The low referral rate and very high level of appropriate referrals could indicate that primary care providers in the public sector played an effective role as gatekeepers in the Malaysian public healthcare system.