One limitation to qualitative research is that, especially to audiences accustomed to reviewing quantitative research, qualitative research may seem to be less than valid in its approach, methods, or conclusions. Qualitative research often depends on the individual judgment of the researcher and is heavily dependent on the researcher's interpretation (for example, in the analysis of interview data or case study information). Although this fact allows for research to reflect the complexity of a particular situation or the knowledge of the researcher, it can also allow the researcher's subjective opinions to bias the information presented or the conclusion drawn. In such cases, the study becomes more reflective of the researcher's opinions than of the actual data, presenting issues with validity.
One significant limitation of qualitative research involves the ability to generalize results to other populations. Because qualitative research is often exploratory and often tailored to the needs of one population (as when a researcher adapts an interview question to a participant's prior knowledge, or when case-study analysis is specific to the person or situation under study), it is difficult to extrapolate findings to more broad populations or to draw general or far-reaching conclusions from the findings of a qualitative study. For example, one might conduct a case study which finds that teachers at a particular school have all articulated a need for more training in technology. Although the findings might be valid for that particular school, it is impossible, from that single case study, to draw a wider conclusion and state that all teachers, everywhere, need more training in technology. Your study, because it is so specific to that school, only indicates something about teachers at that school.
In the same way, qualitative research has limitations with respect to wider or broader implications. Because qualitative research is specific to one setting and is not generalizable, it is difficult or impossible to make broad, sweeping recommendations (such as recommendations for policy change) based on the outcome of the research. To use the example provided in the previous paragraph, one could not use a case study of a single school to formulate a broad policy recommendation to provide all teachers with increased technology training. Because qualitative research provides in-depth answers about one, very specifically defined individual or group, it does not provide assurance that findings can transfer across individuals or groups.
Similar to the challenges surrounding wider implications and generalizable results, qualitative research presents an additional set of issues involving reliability, or the ability to reproduce the study with consistent results. Because qualitative research heavily depends on the researcher's knowledge and interpretation, it is questionable that another researcher, replicating a qualitative study, would achieve the same results -- he might make different decisions about interpretation, might ask interview questions in a different way, or might even change the design halfway through the study, based on perceptions of the participants' needs. This variation can radically change the results of a study and can make study results inconsistent even if two studies have the same approach.