The objectives of this study are to analyze trade patterns between Japan and ASEAN countries during 1988-2003 and analyze the factors that affect both vertical intra-industry trade (VIIT) and low-quality vertical intra-industry trade (LQVIIT) in the selected year 2000. The methods applied The Binary Logistic Model and The Maximum Likelihood Estimation Technique. As for factors determine intra-industry trade, this study had selected to include these variables: GDP-weighted output, Japanese FDI, product number in each industry, difference wage per labor, tariffs and industry dummies which include essentially food, chemicals, wood and pulp products, textiles, metal products, electrical products, transportation equipment and machinery. The results show that exports of ASEAN countries to Japan are mainly low quality products and imports from Japan are mainly high quality products, particularly in Indonesia, Malaysia, the Philippines, Thailand and Vietnam. Singapore is the only exception. The VIIT would occur with the presence of greater GDP-weighted output, Japanese FDI, gap of wage per labor and product number, and lower for higher trade barriers. The selected industries appeared to have higher probability of VIIT as compared to the reference industry e.g. machinery in the case of Singapore. The rest of ASEAN countries appeared to have other kinds of trade patterns because it is shown different values than VIIT. For LQVIIT, the study found that weighted output would promote the kinds of trade patterns found in Indonesia, Singapore and Thailand. On the other hand, Japanese FDI would promote LQVIIT for Indonesia. The study had also found that difference in wage per labor would bring about LQVIIT for Indonesia and Thailand. As for tariffs, the study found that this factor has the probability to obstruct the kinds of LQVIIT to occur in most countries with the exception of Singapore. Finally, the textiles industry looks prominently to have a significant LQVIIT as compared to other industries, especially for countries like Indonesia, Malaysia and Thailand.