The multi-disciplinary nature of Mechatronic Systems (MeSy) results in a highly complex design task, and it is believed that using an integrated approach to design would help reduce this complexity. However, integrated design is hard to implement due to the existing interactions between the components of MeSy. Some of these interactions are referred to as dependencies, and can affect the performance of MeSy while increasing the design task complexity. It is thus necessary to deal with them as early as possible. Although there are some methods to model dependencies, no methods exist to deal specifically with negative effect dependencies. Therefore, we propose a method that enables the identification and assess negative dependencies that exist within a mechatronic system. We first define negative dependencies between two components through four dimensions (affecting level, affected level, effect attenuation and functional closeness) and then assess these dimensions using fuzzy linguistic variables. We then demonstrate the effectiveness of the method by using a quadcopter drone as a case study which shows that it is possible to gain knowledge regarding potential design problems early on.