Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme.Starting with several surprising observations with molecular heterogeneity from recent experiments, we will present how to analyze data with weakly broken ergodicity and what is the possible structural origin of the heterogeneities.Also, to elucidate the consequences of heterogeneous behavior manifested in the single molecule force spectroscopy, we propose an exactly solvable model based on the fluctuating bottleneck model.By fitting our analytical expressions to data from single molecule pulling experiments, we quantify the extent of disorder.