Background Large-scale regeneration programmes to improve the personal conditions and living circumstances in deprived areas may affect health and the lifestyle of the residents. Previous evaluations concluded that a large-scale urban regeneration programme in the Netherlands had some positive effects within 3.5 years. The aim of the current study was to evaluate the effects at the longer run. Methods With a quasi-experimental research design we assessed changes in the prevalence of general health, mental health, physical activity, overweight, obesity, and smoking between the pre-intervention (2003–04 –mid 2008) and intervention period (mid 2008–2013–14) in 40 deprived target districts and comparably deprived control districts. We used the Difference-in-Difference (DiD) to assess programme impact. Additionally, we stratified analyses by sex and by the intensity of the regeneration programme. Results Changes in health and health related behaviours from pre-intervention to the intervention period were about equally large in the target districts as in control districts. DiD impact estimates were inconsistent and not statistically significant. Sex differences in DiD estimates were not consistent or significant. Furthermore, DiD impact estimates were not consistently larger in target districts with more intensive intervention programmes. Conclusion We found no evidence that this Dutch urban regeneration programme had an impact in the longer run on self-reported health and related behaviour at the area level.