Fine particulate matter (PM_2.5) pollution causes serious health disorders, because PM_2.5 becomes deposited in the tracheobronchial and alveoli regions. In the extrathoracic region, there are more deposits of coarse particulate matter than fine particulates. As adverse health issues caused by coarse particulates have not been well investigated, this study examined the cytotoxicity of water-soluble extracts of both fine (0.05–3 µm, PM_0.05–3) and coarse (> 3 µm, PM_>3) particulates collected from April 2016 to March 2019 in Fukuoka, Japan. Also evaluated were concentrations of NH₄⁺ and SO₄²⁻, multi-components of well-known secondary generation substances. The findings revealed that PM_>3 showed stronger cytotoxic effects on mast cell lines than PM_0.05–3. Cytotoxic effects were observed at concentrations of over 15 mM of (NH₄)₂SO₄ and over 30 mM of NH₄Cl. In contrast, Na₂SO₄ caused few cytotoxic effects up to a concentration of 50 mM. The causative substances for this cytotoxicity may not have been NH₄⁺ and SO₄²⁻ because their PM_>3 concentrations indicating the largest cytotoxic effects were 1 and 0.4 mM, respectively. The cytotoxicities of PM_>3 and PM_0.05–3 were the highest in the first half of FY2016. These cytotoxicities seem to be due to cross-border pollution, although this pollution has been declining in recent years. An increasing trend of cytotoxicity was observed in the second half of FY2018. This study showed that cytotoxicity and particulate concentrations are not always correlated. Thus, we should focus not only on the quantity of atmospheric particulate matter, but also on its quality.