The aim of this study was to determine the incidence and risk factors for early lactation problems [suboptimal infant breastfeeding behaviour (SIBB), delayed onset of lactogenesis (OL) and excessive neonatal weight loss] among mother–infant pairs in Lima, Peru. All primiparous mothers who gave birth to a healthy, single, term infant at a government hospital in a peri-urban area of Lima during the 8-month recruitment period were invited to participate in the study. Data were collected at the hospital (day 0) and during a home visit (day 3). Infant breastfeeding behaviour was evaluated using the Infant Breastfeeding Assessment Tool; SIBB was defined as ≤10 score. OL was determined by maternal report of breast fullness changes; delayed OL was defined as perceived after 72 h. Excessive neonatal weight loss was defined as ≥10% of birthweight by day 3. One hundred seventy-one mother–infant pairs participated in the study. SIBB prevalence was 52% on day 0 and 21% on day 3; it was associated with male infant gender (day 0), <8 breastfeeds during the first 24 h (days 0 and 3), and gestational age <39 weeks (day 3). Delayed OL incidence was 17% and was associated with infant Apgar score <8. Excessive neonatal weight loss occurred in 10% of neonates and was associated with maternal overweight and Caesarean-section delivery. Early lactation problems may be influenced by modifiable factors such as delivery mode and breastfeeding frequency. Infant status at birth and maternal characteristics could indicate when breastfeeding dyads need extra support.