Social networking is expanding in the Middle East including Palestine where alternative social opportunities and leisure time activities are limited due to cultural norms and geopolitical realities. Health consequences of excessive use are of concern. The aim of this study is to assess the unhealthy habits and physical health complaints in relation to the level of Facebook use in university students in Palestine. A cross-sectional design was used to investigate the effects of excessive Facebook use on healthy habits and negative health consequences of Palestinian university students. Nine hundred twenty-two students completed a self-administered questionnaire that assessed demographics, patterns of Facebook use, unhealthy habits and adverse physical health. Facebook use was evaluated using the Facebook Intensity Scale (FIS). Among the students, 389 (42%) reported using Facebook till midnight or later and 390 (42.4%) felt it affected their sleep patterns. 478 (51.8%) noticed that they have lower daily energy levels than before joining Facebook. Additionally, 477 (51.0%) said that they dedicated less time for physical exercise than before. A positive relationship was found between time spent on social network sites, number of Facebook friends, and Facebook Intensity Scales scores and an increase in unhealthy habits including skipping meals (p= <0.001), holding urination (p= <0.001), late night and interrupted sleep (p= <0.001). Negative health consequences related to excessive use included eye strain (p= <0.001), reduction in frequency and duration of exercise (p= <0.001), as well as back and wrist pain (p= <0.001). Excessive social networking is associated with unhealthy habits and negative health effects on the student population. Public awareness and alternative opportunities for socialization and recreation are needed.