Flexible working hours can have several meanings and can be arranged in a number of ways to suit the worker and/or employer. Two aspects of "flexible" arrangement of working hours were considered: one more subjected to company control and decision (variability) and one more connected to individual discretion and autonomy (flexibility). The aim of the study was to analyze these two dimensions in relation to health and well-being, taking into consideration the interaction with some relevant background variables related to demographics plus working and social conditions. The dataset of the Third European Survey on working conditions, conducted in 2000 and involving 21,505 workers, was used. Nineteen health disorders and four psycho-social conditions were tested by means of multiple logistic regression analysis, in which mutually adjusted odds ratios were calculated for age, gender, marital status, number of children, occupation, mode of employment, shift work, night work, time pressure, mental and physical workload, job satisfaction, and participation in work organization. The flexibility and variability of working hours appeared inversely related to health and psycho-social well-being: the most favorable effects were associated with higher flexibility and lower variability. The analysis of the interactions with the twelve intervening variables showed that physical work, age, and flexibility are the three most important factors affecting health and well-being. Flexibility resulted as the most important factor to influence work satisfaction; the second to affect family and social commitment and the ability to do the same job when 60 years old, as well as trauma, overall fatigue, irritability, and headache; and the third to influence heart disease, stomachache, anxiety, injury, and the feeling that health being at risk because of work. Variability was the third most important factor influencing family and social commitments. Moreover, shift and night work confirmed to have a significant influence on sleep, digestive and cardiovascular troubles, as well and health and safety at work. Time pressure also showed a relevant influence, both on individual stress and social life. Therefore, suitable arrangements of flexible working time, aimed at supporting workers' coping strategies, appear to have a clear beneficial effect on worker health and well-being, with positive consequences also at the company and social level, as evidenced by the higher "feeling to be able to work until 60 years of age".