Main purpose of this research paper is to show the recent trends of labour market issues regarding gender inequality in the countries that are still in the transition to the market oriented economy. Transition to competition has effected in increasing the level of unemployment to economically active population, with the higher consequence for females than for males, from which some females have left labour market and they became inactive in job searching. In this paper we analyze and compare gender gaps through the main components of labour market trends as level of education, active participation in labour market, occupational segregation, employment and unemployment for both genders of the countries that are still in transition like Albania, FYR of Macedonia and Kosovo in comparison with EU countries. Given that closer are these countries in joining the EU; higher are the requirements for increasing the level of employment targets and in approving and implementing social policies on gender equality in labour market according to the EU legislations. Methodology used in this paper is through case studies by using secondary data from the most recent labour force surveys (LFS) of transition countries in South East Europe and comparing them with the EU targets. Also regarding occupational segregation by gender the Duncan & Duncan Index is calculated. The study shows that depending on the stages that countries are in transition earlier or latter, the labour market components regarding gender are more comparable and closer with the targets of the EU countries, and that occupational segregation is higher in the transition countries where the unemployment level of females is in the higher range.