Microbiological analysis of teeth with chronic apical periodontitis and the outcome of treatment by gutta percha points impregnated with either calcium hydroxide or chlorhexidine as intra canal medicament Bacteria have a major role in the success of an endodontic treatment. Mechanical preparation alone cannot effectively eliminate bacteria from dentinal tubules and other irregularities in the root canal. Few remnant microorganisms can multiply between appointments often reaching the same level as at the start of the previous session. These observations call for an effective intracanal medication that will help to disinfect the root canal system. Calcium hydroxide has an antibacterial effect on most of the endodontic pathogens. This is due to its high alkalinity. It damages the bacterial cytoplasmic membrane. Chlorhexidine has been found to have a broad-spectrum antimicrobial action and relative absence of toxicity. Calcium hydroxide points as well as chlorhexidine gutta percha points are ready to be used in a flexible way and easily to be introduced into the canal. Three bacterial cultures -before, after instrumentation and after medication by either one of the experimental materials -were taken from forty healthy patients having non-vital single rooted teeth with chronic apical periodontitis. Twelve types of bacteria were commonly isolated with different frequencies. Anaerobes represented about 56.1 % and aerobes represented about 43.9 % of the total bacteria. Streptococcus mitis (15.2 %) was the most frequent isolated bacteria (aerobes and anaerobes) from all the cases in the 1st culture. Then it was followed by Prevotella intermedia (14.7 %), Peptostreptococcus spp. (10.5%), Eubacterium lentum (9.4 %), Lactobacillus spp. (8.9 %), Staphylococcus aureus (8.4 %), Veillonella parvula (7.9 %), Enterococcus faecalis (7.3 %), Escherichia coli (E-coli) (6.8 %), Neisseria catarrhalis (5.2 %), Proionibacterium spp. (4.7 %), Staphylococcus epidermis (1 %). The results demonstrated a highly significant reduction in the bacterial growth in the experimental groups before and after instrumentation and medication of the root canal when compared to the control. Chlorhexidine gutta percha points proved to have a significant better antibacterial effect than calcium hydroxide gutta percha points.