Common side effects of doxycycline include gastrointestinal disturbances such as nausea, vomiting, diarrhea, and abdominal pain. Photosensitivity is another notable side effect, where patients may experience an exaggerated sunburn reaction upon exposure to sunlight. Long-term use can lead to superinfection with resistant organisms or fungi. It is important to monitor patients for these side effects, especially in prolonged treatments.