BackgroundSeventy-five percent of the population in Europe live in urban areas and analysing the effects of urban form on the health of the urban population is of great public health interest. Not much is known, however, on the effects of urban form on the health of city dwellers. This study uses a novel approach to investigate whether associations exist between different measures of urban form and mortality risks in cities in England.MethodsWe conducted an ecological, cross-sectional study for urban areas in England with more than 100,000 residents (n = 50) and included all registered premature deaths (<65 years) between 1st January 2002 and 31st December 2009. To describe and categorise urban form we quantified the distribution and density of population, land cover and transport networks and measures of geographical characteristics. We used Poisson regression models to examine associations between the measures of urban form and age-standardised risks of deaths from all causes, cardiovascular disease, and traffic accidents after adjustment for socioeconomic status and smoking. Analysis was stratified by gender to explore differential associations between females and males.ResultsThere were a total of 200,200 premature deaths during the study period (Females: 37 %; Males: 63 %). Transport network patterns were associated with overall and cardiovascular mortality rates in cities. We saw 12 % higher mortality risk after adjustment in cities with high junction density compared to cities with low density [Females: RR 1.12 (95 % CI 1.10 – 1.15); Males: RR 1.12 (95 % CI 1.10–1.14)]; the risk was slightly higher for cardiovascular mortality [Females: RR 1.16 (95 % CI 1.10 – 1.22); Males: RR 1.12 (95 % CI 1.09 – 1.16)]. Associations between mortality and population patterns were of similar magnitude [Females: RR 1.10 (95 % CI 1.09 – 1.13); Males: RR 1.09 (95 % CI 1.07–1.10)]; associations between mortality and land cover patterns were inconclusive.ConclusionsWe found an association between transport patterns and risk of premature mortality. Associations between urban form and mortality observed in this study suggest that characteristics of city structure might have negative effects on the overall health of urban communities. Future urban planning and regeneration strategies can benefit from such knowledge to promote a healthy living environment for an increasing urban population.Electronic supplementary materialThe online version of this article (doi:10.1186/s12940-016-0106-3) contains supplementary material, which is available to authorized users.