Cycling as a mode of travel provides an opportunity for many people to increase their levels of regular physical activity and contribute to their mental and physical health. Heart rate is often used as a means of measuring the intensity and energy expenditure of physical activity. However, heart rate is also linked to emotional factors such as anxiety and fear. Perceptions of risk due to external factors such as other road users and infrastructure may arouse such emotions in urban cyclists. The present study set out to investigate whether or not perceptions of risk among urban cyclists may lead to increased heart rates. Cyclists completed a test route in normal traffic conditions in Cork, Ireland and heart rates and self-reported risk ratings were recorded in real time. Evidence was found of a link between perceptions of risk and heart rates. This raises questions regarding the use of heart rate to estimate exercise intensity and energy expenditure during urban cycling. The perceptions of cyclists of their safety in relation to various road elements on familiar routes were also assessed, as well as specific events which they perceive to be high in risk. The results indicate that incidents involving car traffic and busy roads which offer no protection from interaction with car traffic are associated with greatest perceptions of risk.