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Events such as vaginitis (can lead to vaginal discharge, odor), headache, back ache, lethargy have been observed in less than 1 % of ciprofloxacin patients. (Ref: http://www.rxlist.com/cgi/generic/cipro_ad.htm)
It is difficult to say if they are due to the underlying disease or due to ciprofloxacin. You should consult your doctor for a complete evaluation and diagnosis.
Regards
How are you? Common side effects of ciprofloxacin are stomach pain, headache, vomiting, diarrhea, stomach upset and restlessness. Rarely it can cause skin sensitivity to sunlight, rash, breathing difficulty etc.
Vaginal discharge with odour and back pain are the manifestations of UTI. Since how long are you using ciprofloxacin?
Feel free to ask if you have any more doubts.
Take care.