Background The health effects of short-term exposure to ambient ultrafine particles in micro-environments are still under investigation. Methods Sixty-four individuals with type 2 diabetes and impaired glucose tolerance recorded ambulatory electrocardiograms over five to six hours on 191 occasions in a panel study in Augsburg, Germany. Personal exposure to particle number concentrations (PNC) was monitored for each individual on 5-minute basis concurrently and particulate matter with an aerodynamic diameter < 2.5 μm (PM2.5) was acquired from a central monitoring site on an hourly basis. Results More than 11,000 5-minute intervals were available for heart rate and measures of heart rate variability including SDNN (standard deviation of NN intervals). A concurrent decrease in 5-minute SDNN of −0.56% (95% confidence limits (CI): −1.02%; −0.09%) and a 5-minute delayed increase in heart rate of 0.23 % (95% CI: 0.11%; 0.36%) was observed with an increase in personal PNC of 16,000 per cm3 in additive mixed models. Models evaluating the association of concurrent 5-minute personal PNC and of 1-hour PM2.5 showed independent effects on SDNN. Conclusion The data suggest that freshly emitted ultrafine particles and aged fine particulate matter are both associated with changes in cardiac function in individuals with type 2 diabetes and impaired glucose tolerance in urban areas.