BACKGROUND The purpose of this population-based registry study was to analyze both birth-related femur and humerus shaft fractures and diagnosed later in infancy, as regards incidence, perinatal characteristics, other diagnoses, and reported accidents. METHODS Children born in 1997-2014, diagnosed with a femur or humerus shaft fracture before age 1 year, were identified in the Swedish Health Registries. Rate of birth fractures were estimated by combining femur and humerus shaft fractures coded as birth-related with femur and humerus shaft fractures diagnosed during day 1-7 without registered trauma or abuse. Incidence was computed by comparing infants with femur or humerus shaft fractures to the total at-risk population. RESULTS The incidence for birth-related femur shaft fractures was 0.024 per 1000 children (n = 45) and that for birth-related humerus shaft fractures was 0.101 per 1000 children (n = 188). The incidence was 0.154 per 1000 children for later femur shaft fractures (n = 287) and 0.073 per 1000 children for later humerus shaft fractures (n = 142). Birth-related femur shaft fracture was associated with shoulder dystocia, cesarean, multiple birth, breech, preterm, and small-for-gestational age, while humerus shaft fracture was associated with maternal obesity, dystocic labor, shoulder dystocia, vacuum-assisted delivery, male sex, multiple birth, breech, preterm, large-for-gestational age, birth weight > 4000 g, and injury of brachial plexus. A bone fragility diagnosis was recorded in 5% of those with birth-related or later femur shaft fractures. Among infants with birth-related humerus shaft fractures, 1% had a bone fragility diagnosis; the figure for later fractures was 6%. Maltreatment diagnosis was associated with later fractures of both types, especially among those aged < 6 months, where approximately 20% (femur) and 14% (humerus) of cases, respectively, were associated with abuse. Fall accidents were reported in 73 and 56% among those with later femur and humerus shaft fractures, respectively. CONCLUSIONS This study provides data on epidemiology, birth, parental characteristics, and reported accidents in relation to femur and humerus shaft fractures during infancy. Few children had a bone fragility diagnosis. Fall accidents were the main contributor to femur or humerus shaft fracture during infancy; however, the proportion of fractures attributed to maltreatment was high in children under 6 months.