Background: One of the most common reasons why females attend doctor are vaginal infections. Vaginal flora is a dynamic environment where a great variety of microorganisms exist in homeostasis. The main normal flora inhabitants are Lactobacillus species who protect from pathogens. Still the majority of factors remain unclear about this genteel environment and its interaction. Aim & Objectives: to analyze vaginal microflora types and microbial species in pregnant women, who were at their first trimester, using PCR and Nugent score diagnostic methods. Methods: 65 pregnant women before their 12th week of pregnancy participated in this study from 06.08.2012 till 31.01.2013. All participants were divided in to 2 groups, group A (n=45) normal pH and group B (n=20) pH ( ≥4,5). Their vaginal fluid were analysed with Nugent score and PCR methods. Results: Genus Lactobacillus (any Lactobacillus) was detected by PCR in all women irrespective of Nugent score, most common species were L. crispatus, L. jensenii, and L. inners, less common were L. gasseri, L. plantaris, L. rhamnosus and L. reuteri. G. vaginalis was present in both patient groups divided by pH but it was significantly higher in bacterial vaginosis and intermediate flora group detected by Nugent score and group B (high pH group). Megasphaera, Leptotrichia/Sneathia were detected more common in pathogenic flora than normal flora. A. vaginae finding was associated with pathologic flora. Conclusion: The most common isolated species in pregnant women vaginal flora were L. crispatus, L. jensenii, and L. inners. L. gasseri and L. plantaris were second most often found species. L. jensenii detection was significantly higher in normal flora group. A. vaginae were mainly detected in patients with bacterial vaginosis. Megasphera and Leptotrichia/Sneathia are more common for patients with pathologic flora. PCR method is the most precise to identify microorganisms in vaginal flora but rather expensive and time consuming than vaginal fluid examination by Nugent score