Preventing more environmental issues and relieving reliance on fossil fuels motivate the governments and policy-makers to encourage people to use more efficient and qualified electric vehicles (EVs), in comparison with conventional vehicles. As all or portion of EVs energy is supplied from secondary distribution system, uncontrolled and simultaneous charging of them would cause serious operational issues for secondary distribution systems. Some of the common issues in the secondary distribution system operation are the power, current and voltage imbalances. Increased losses, increased current in neutral wires and shift in neutral point are the results of the imbalance issue. This issue can be exacerbated by uncontrolled EVs charging. This challenge could change to a bottleneck in penetrating EVs into the distribution system and should be resolved. Therefore, an EVs charging coordination framework is required. Another common issue in secondary distribution system operation is the harmonic pollution. Although from the power quality point of view, the two mentioned issues are treated differently, resolving imbalance challenge cannot be achieved without considering harmonic pollution; since these two issues have the same impacts on losses, current in neutral wires and shift in neutral point. Therefore, the EVs charging coordination framework should be designed in such a way that the imbalance and harmonic issues are jointly addressed in. Interface between EV battery and secondary distribution system is battery charger that is a power electronic-based device. These devices can easily control active and reactive power flow of the charger as well as harmonics of injected current. In this research we consider single-phase and three-phase charging systems, simultaneously, equipped with mentioned control capabilities. Moreover, we assume that power transfer between phases in the three-phase charging systems are possible. To communicate with EV charging systems, we consider that a smart communication infrastructure is provided by the distribution system operator. Based on this assumptions, EVs charging coordination problem is modeled as an optimization problem with voltage imbalances and harmonic pollution minimization as the joint objective function. The model constraints consist of harmonic power flow equations, EVs constraints and distribution system operational constraints. In order to reduce solving time and achieve global optimum, nonlinear terms are linearized using some linearization techniques. Therefore, the optimization model is recast as a linear optimization problem. The proposed model is implemented in a 39-bus test system and the numerical results are provided and analyzed. As, in practice some of the input parameters are stochastic, the proposed deterministic optimization model is developed to a stochastic optimization model. Residential load profile, arrival and departure time of EVs, and the battery state of charge when the EVs are plugged into the distribution system are stochastic parameters that are considered. The proposed stochastic optimization model is implemented in the 39-bus test system and the numerical results are provided and analyzed. The numerical results show the efficiency and efficacy of the proposed models in improving the operational conditions of secondary distribution networks. Keywords: Electric vehicles, Charging coordination, Secondry distribution system, Imbalance, Harmonic pollution.