Urinary tract infection (UTI) is a common childhood infection. Many febrile children require a urine sample to diagnose or exclude UTI. Collecting urine from young children can be time-consuming, unsuccessful or contaminated. Cost-effectiveness of each collection method in the emergency department is unknown. To determine the cost-effectiveness of urine collection methods for precontinent children. A cost-effectiveness analysis was conducted comparing non-invasive (urine bag, clean catch and 5 min voiding stimulation for clean catch) and invasive (catheterisation and suprapubic aspirate (SPA)) collection methods, for children aged 0-24 months in the emergency department. Costs included equipment, staff time and hospital bed occupancy. If initial collection attempts were unsuccessful subsequent collection using catheterisation was assumed. The final outcome was a definitive sample incorporating progressive dipstick, culture and contamination results. Average costs and outcomes were calculated for initial collection attempts and obtaining a definitive sample. One-way and probabilistic sensitivity analyses were performed. For initial collection attempts, catheterisation had the lowest cost per successful collection (GBP£25.98) compared with SPA (£37.80), voiding stimulation (£41.32), clean catch (£52.84) and urine bag (£92.60). For definitive collection, catheterisation had the lowest cost per definitive sample (£49.39) compared with SPA (£51.84), voiding stimulation (£52.25), clean catch (£64.82) and urine bag (£112.28). Time occupying a hospital bed was the most significant determinant of cost. Catheterisation is the most cost-effective urine collection method, and voiding stimulation is the most cost-effective non-invasive method. Urine bags are the most expensive method. Although clinical factors influence choice of method, considering cost-effectiveness for this common procedure has potential for significant aggregate savings.