Variation Order (VO) is a common phenomenon in construction projects. It involves an amendment of the original scope of work as in the contract. VO is caused from various factors. Variations often cause disputes and dissatisfactions among the parties involved in construction projects. Thus, it is very important to control VOs in a construction project. For this, the first step is to uncover and understand the causes and effects of VO. Hence, the aim of this study is to determine the significant causes and effects of VO in construction projects. Data collection involved the survey with a structured questionnaire consisting of 18 causes and 9 effects of variation orders identified through comprehensive literature review. Survey was carried out among client representatives, consultants and contractors involved in handling projects of Malaysian Public Works Department (PWD) known as Jabatan Kerja Raya Malaysia (JKR). A total of 101 completed questionnaire sets were collected against 200 questionnaires distributed among the practitioners. Collected questionnaires were analyzed with statistical software package SPSS and Average Index formula. The results of the study showed that in Malaysia's JKR projects often variation orders are occurred; these VO's are majorly caused because of unavailability of equipment, poor workmanship and design complexity. While most significant effects of VO on the projects are increased project cost, delay in completion and logistic delays. Early participation of professionals may be beneficial in reducing the occurrence of variations. Also, improved design and avoiding frequent design changes will be very effective in controlling the problem of variations.