The purposes of this study are to examine the effect of complex accounting estimates on  audit fees and the role of audit committee’s effectiveness and family ownership as moderating variables. This research uses sample of Indonesia Stock Exchange non-financial companies from the years 2011-2015. The complex accounting estimates used in this study are non-financial assets revaluation, goodwill and goodwill-impairment. Regression results show that revaluation of non-financial assets, goodwill and goodwill-impairment have no effect on audit fee. However, the moderating effect of the audit committees’ effectiveness and family ownership have negative effect on the influence of non-financial asset revaluation on audit fees. The results of this study can be used as a reference for regulators to set auditing standards related to fair value audit procedures that require complex accounting estimates, so that auditors are more aware of the reliability of fair values ​​that are difficult to observe.