With increasing bit-rate polarization mode dispersion (PMD) is becoming major system impairment. As the birefringence of a fiber changes randomly along a fiber link and the state-of-polarization (SOP) of an optical signal changes with environmental conditions, PMD effects on the data signal are stochastic and time varying. Consequently analysis of impairment caused by PMD is difficult. In order to assess the PMD impairment in optical transmission system, a great many of samples of the systems under different conditions have been studied previously. The former studies have been shown that PMD-induced system impairment depend on many transmission factors, such as modulation formats, receiver characteristics, etc. Recently the effects of transmission characteristics on PMD impairments have been taken into account. In this paper, we take these effects into account together for the first time to our knowledge. Firstly we show in both experiments and simulations that the imperfection of transmitters, primarily timing and amplitude jitters, could significantly increase the PMD-induced penalty in optical fiber transmission systems, especially when the instantaneous DGD is large, which is relevant situation for outage occurrence. Then we introduce a novel method to analyze the effects of transmission and transmitter imperfection on PMD impairments synthetically. Furthermore, we try to establish a new standard of estimating the PMD impairments.