Background: In 2003 the Afghan Ministry of Public Health (MoPH) adopted the Integrated Management of Childhood Illness (IMCI) for delivering child health services in primary care facilities. Key problems were subsequently identified: high cost of training, frequent health worker turnover and poor quality of IMCI implementation by those trained -specifically in the use of job aids and protocols for assessment, classification, treatment and counselling. The high financial, human resources and opportunity costs of implementing IMCI spurred the MoPH to prioritize developing a shortened IMCI course of comparable quality to the 11-Day training. Methods: This cross-sectional evaluation compared knowledge before and after training, and health worker performance in assessment, classification and treatment of sick children in two similar cohorts, eight months post-training. Results: The mean increase in knowledge scores of the thirty 7-Day course trainees was 29 [95% Confidence Interval (CI): 24, 34] compared to 23 (95% CI: 18, 28) in the 31 trained in the 11-Day course. During assessment visits, mean scores in the 7-Day course trainees and the 11-Day course trainees were 93% (95% CI: 91, 95) versus 94% (95% CI: 91, 96) in assessment; 95% (95% CI: 89, 100) versus 96% (95% CI: 91, 100) in classification; 95% (95% CI: 92, 100) versus 97% (95% CI: 95, 100) in treatment; and 81% (95% CI: 76, 86) versus 80% (95% CI: 75, 85) in counselling. The 7-Day course was 36% less expensive than the 11-Day course. For each course opportunity costs, measured as numbers of children who potentially received poorer care than usual during trainee absence, were 3,160 for the 11-Day course and 2,016 for the 7-Day course. This measure was chosen because trainee absence commonly resulted in higher patient volumes per remaining provider or complete closure of a health facility with one single health worker. Conclusion: Given similar performance and knowledge of health workers trained in both courses, potential cost savings, the possibility of training more health workers and the relative ease with which health workers in remote settings might participate in a shorter course, it seems prudent to standardize the 7-Day course in Afghanistan where child mortality rates remain unacceptably high.