INTRODUCTION: Previous studies in the public sector in Uganda have demonstrated major prescribing problems due to polypharmacy and irrational use of antibiotics and injections. Little is known about prescribing in the private sector although there is little government regulation influencing practice in this sector. The introduction of policies such as the Uganda National Standard Treatment Guidelines (UNSTG) was expected to improve prescribing practices in the public and private sectors. This paper measures appropriateness of prescribing practices in the public and private sectors in Uganda for the treatment of Acute Respiratory Infections (ARI) and malaria in adult patients. DESIGN AND SAMPLING: We combined a prospective survey of treatment for simulated patients presenting with symptoms of malaria and ARI in 119 randomly selected private clinics and a retrospective survey of 600 prescription records for malaria and ARI (300 for each condition) randomly selected from 10 public health units in the Kampala, Masaka, and Jinja urban areas. OUTCOME MEASURES: Percentage of drug appropriately prescribed in each condition, % injection prescription, percentage antibiotic prescription, average number of drugs per case, average standardized cost per prescription, distribution of types of drugs prescribed. RESULTS: The overall appropriateness of prescribing for ARI and malaria was poor in both public and private sectors. Treatment of malaria was significantly less appropriate in the public sector compared to the private sector (14% vs. 27%, p = 0.002), with injectable chloroquine much more commonly prescribed. Prescribing of antibiotics for ARI was nearly universal in both sectors, with some prescriptions containing up to three antibiotics; newer, more expensive antibiotics were more commonly prescribed in the private sector. Polypharmacy and unnecessary prescribing of vitamins were common in both conditions and both sectors. CONCLUSIONS: Prescribing for adult malaria and ARI by both private and public practitioners did not conform to the UNSTGs. Although practitioners were largely the same in both sectors, prescribing practices often differed dramatically. The extent of inappropriate prescribing in both sectors calls for in-depth investigation of the system factors and motivations that underlie problem practices, and the development of interventions that target these causative factors.