This study aims to determine the level of understanding on the basic steps of scientific method using mother tongue of the grade 4 pupils of Minolos Elementary School and Maria Montessori School. The pupils of MES are purely Cebuano who communicate Visaya or Cebuano at home while the pupils of MMIS are a mix of Cebuano, American, and Korean. Majority of the pupils in MMIS use English at home. Post-test design is used as indicated in the methodology. The questions focus on hypothesis making, data gathering, data interpretation and conclusion formulation. The questions are constructed in English. Paired sample T-test is used to determine the relationship of the types of language used. The result of the study showed that the mean score of MES is greater than MMIS. Moreover, it showed that there is no significant difference between the Cebuano-English and Pure English medium of instruction in understanding the steps of the Scientific Method. This means that although language plays a role in the classroom, pupils should be given opportunity to actually experience learning especially in a subject that requires investigation. Effective communication and student interaction are important in a Science class.