As a systematic process for gathering and analyzing data, performance evaluation could be used as a valid method to highlight levels of success and to identify strength and weakness of ongoing programs. The aim of the present study was to develop an instrument for evaluating rural health centers in Iran. Based on related literature and experts’ views, eight crucial fields of performance evaluation, and a questionnaire including 100 items were formed. The participants of the study were 525 people having health related jobs in rural or urban health centers. Reliability and validity requirements were checked; exploratory and confirmatory factor analyses were used. Factor analysis identified 11 components which embraced 60 items. Components were named as planning, control, coordination, structure, setting and facilities, education, customers’ satisfaction, staff’s job satisfaction, disease surveillance, mother-child care, and effectiveness which are presented as a model for performance evaluation. The obtained instrument embraces all required factors suggested by experts and literature hence it can be used as an evaluation instrument in both rural and urban health centers.