well i asked this question a few weeks ago and was told that they can stay in your body for to a week after finishing the course. Im not a doctor so dont take my word 4 it thou :). It depends on the specific antibiotic. The half-lives vary. Name one. I just had a relative with pneumonia, and the doctor gave him a strong (5 day)antibiotic, and said it would stay in his body for several days after he finished his last dose. This came straight from the doctor, so that's reliable. Most antibiotics are designed to stay in your system at a therapeutic level for 7 to 10 days. That means that they are actually killing bacteria. However, the effects on your body after finishing the full course of the drug, can last up to 6 months.