Objective: To analyse characteristics and prognostic value of HPV status (human papilloma virus), HPV 16 genotype and cytomorphology in the patients with cervical cytology finding of borderline and mild abnormalities of squamous epithelium. Material and methods: Patients with initial cytology finding of atypical squamous cells of undetermined significance (ASCUS, N = 160) and low-grade squamous intraepithelial lesion (LSIL, N = 155) were included. Cytomorphological characteristics of koilocytosis, parakeratosis and macrocytosis were analysed. In all patients HPV DNA test was performed using high risk probe of hybrid capture 2 test. In positive samples additional HPV genotyping was doneusing INNO-LiPA HPV Genotyping v2 assay. Patients were followed by cytology, colposcopy and histology for average of 26 months. Three possible clinical outcomes: regression, stagnation or progression were recorded. Results: The most frequent HPV genotype was HPV 16 and it was found in 27.9% ASCUS (N = 29) and in 16.5% LSIL (N = 16) cases. It was found more frequently in women under 30 years of age (P < 0.001). Macrocytosis was more frequent finding in HR HPV negative cases in ASCUS and LSIL (P < 0.05). Koilocytosis and parakeratosis did not show relationship with HR HPV status. When analysed according to HPV genotype, in LSIL, koilocytosis was more frequent finding in HPV non-16 genotype compared to HPV 16 genotype (P=0.002). Parakeratosis is more frequently found in HPV non-16 genotype cases, but statistically significant difference is found only in LSIL (P = 0.005). Unfavourable disease outcome was recorded in 25.3% of ASCUS and 13.8% LSIL. Disease progression was associated with HR HPV positivity (P < 0.001) and HPV 16 genotype (P < 0.001). Presence of koilocytosis, parakeratosis and macrocytosis are not associated with the unfavourable disease outcome in ASCUS and LSIL. Conclusion: HPV 16 was the most frequent genotype in ASCUS and LSIL and it is more frequently associated with koilocytosis and parakeratosis absence. HR HPV DNA positivity and HPV 16 genotype were associated with the disease progression in ASCUS and LSIL. Cytomorphology features showed no association with the unfavourable disease outcome. These results could help in optimising follow up and management of patients with initial cytology diagnosis of ASCUS and LSIL and have possible impact on used guidelines for cervical abnormalities.