Two experiments used eye-tracking during reading to investigate the role of the consistency of the relative markedness alignment of noun phrases (NPs) in the processing of complex sentences in Korean. To do so, the animacy of the first NP was varied in both experiments to manipulate the relative markedness of NPs. In addition, case markings of the second NP (nominative vs. accusative) were manipulated in the first experiment and the markings of the first NP (nominative vs. topic) were manipulated in the second experiment. Results revealed that the animacy manipulation and the nominative-topicality manipulation showed measurable influence on the participants' reading of the complex sentences. Also, the effect of the prominence misalignment caused by animacy seems to have a stronger effect on reading than the effect caused by the nominative-topicality manipulation. The experiments suggested that on-line processing of Korean complex sentences are affected by the consistency of the relative markedness alignment of NPs.