Doxycycline, like all antibiotics, may cause diarrhea in your dog, and doxycycline makes your pet's skin more vulnerable to sunburn, particularly on exposed areas of the body like the nose, and in short-haired or white dogs. Your dog may urinate less or have darker colored urine while taking doxycycline. Some dogs will experience an allergic reaction after taking doxycycline - they may have difficulty breathing or experience facial and throat swelling. Other possible side effects include headaches, jaundice, and liquid-filled vesicles around the groin, mouth or ears. If you notice any adverse reactions to doxycycline while your pet is taking it, contact your veterinarian right away.