Abstract Background Optimal clinical management of childhood urinary tract infections (UTI) potentiates long-term positive health effects. Insight into the quality of care in Dutch family practices for UTIs was limited, particularly regarding observation periods of more than a year. Our aim was to describe the clinical management of young children's UTIs in Dutch primary care and to compare this to the national guideline recommendations. Methods In this cohort study, all 0 to 6-year-old children with a diagnosed UTI in 2001 were identified within the Netherlands Information Network of General Practitioners (LINH), which comprises 120 practices. From the Dutch guideline on urinary tract infections, seven indicators were derived, on prescription, follow-up, and referral. Results Of the 284 children with UTI who could be followed for three years, 183 (64%) were registered to have had one cystitis episode, 52 (18%) had two episodes, and 43 (15%) had three or more episodes. Another six children were registered to have had one or two episodes of acute pyelonephritis. Overall, antibiotics were prescribed for 66% of the children having had ≤ 3 cystitis episodes, two-thirds of whom received the antibiotics of first choice. About 30% of all episodes were followed up in general practice. Thirty-eight children were referred (14%), mostly to a paediatrician (76%). Less than one-third of the children who should have been referred was actually referred. Conclusion Treatment of childhood UTIs in Dutch family practice should be improved with respect to prescription, follow-up, and referral. Quality improvement should address the low incidence of urinary tract infections in children in family practice.