Clinic-based recruitment for preventative interventions for child health may select for healthier populations compared with community-based outreach. Nutritional status during infancy as measured by anthropometry is predictive of mortality, growth faltering later in life, and poor cognitive development outcomes. We evaluated baseline differences in infant nutritional status among children recruited directly in their community versus clinic recruitment among infants participating in a trial of azithromycin compared with placebo for prevention of mortality in three districts of Burkina Faso. Infants between 5 and 12 weeks of age were recruited in their community of residence via vaccine outreach teams or in primary health-care clinics during vaccine clinics. Weight, height, and mid upper arm circumference were measured. We used linear and logistic regression models to compare anthropometric outcomes among community and clinic recruited infants, adjusting for age at enrollment, gender, and season. Among 32,877 infants enrolled in the trial, 21,273 (64.7%) were recruited via community outreach. Mean weight-for-age z-score (WAZ) was -0.60 ± 1.2 (SD), weight-for-length z-score (WLZ) was -0.16 ± 1.5, and length-for-age z-score was-0.53 ± 1.3. Infants enrolled in the community had lower WAZ (mean difference, -0.12; 95% CI, -0.20 to -0.04) and WLZ (mean difference, -0.21; 95% CI, -0.32 to -0.09). Community-recruited infants were more often underweight (WAZ < -2; odds ratio [OR], 1.25; 95% CI, 1.09-1.43) and wasted (WLZ < -2; OR, 1.54; 95% CI, 1.31-1.79). There was no evidence of a difference in height-based measures. Community and clinic recruitment likely reach different populations of children.