* High energy costs currently associated with generating and transporting hydrogen offsite.
* Presently generated from natural gas still dependent on fossil fuels (although any combustible hydrocarbon can be used).
* Production from biomass is highly land-intensive 
* Energy density (by weight or volume) one half of that of gasoline and 24% less than ethanol
* Handling
** If no inhibitors are used, methanol is corrosive to some common metals including aluminum, zinc and manganese. Parts of the engine fuel-intake systems are made from aluminum. Similar to ethanol, compatible material for fuel tanks, gasket and engine intake have to be used.
** As with similarly corrosive and hydrophilic ethanol, existing pipelines designed for petroleum products cannot handle methanol. Thus methanol requires shipment at higher energy cost in trucks and trains, until new pipeline infrastructure can be built, or existing pipelines are retrofitted for methanol transport.
** Methanol, as an alcohol, increases the permeability of some plastics to fuel vapors (e.g. high-density polyethylene).  This property of methanol has the possibility of increasing emissions of volatile organic compounds (VOCs) from fuel, which contributes to increased tropospheric ozone and possibly human exposure.
* Low volatility in cold weather: pure methanol-fueled engines can be difficult to start, and they run inefficiently until warmed up. This is why a mixture containing 85% methanol and 15% gasoline called M85 is generally used in ICEs. The gasoline allows the engine to start even at lower temperatures.
* With the exception of low level exposure, methanol is toxic. Methanol is lethal when ingested in larger amounts (30 to 100 mL). But so are most motor fuels, including gasoline (120 to 300 mL) and diesel fuel. Gasoline also contains small amounts of many compounds known to be carcinogenic (e.g. benzene). Methanol is not a carcinogen, nor does it contain carcinogens. However, methanol may be metabolized in the body to formaldehyde, which is both toxic and carcinogenic.  Methanol occurs naturally in small quantities in the human body and in edible fruits.
* Methanol is a liquid: this creates a greater fire risk compared to hydrogen in open spaces as Methanol leaks do not dissipate. Methanol burns invisibly unlike gasoline. Compared to gasoline, however, methanol is much safer. It is more difficult to ignite and releases less heat when it burns. Methanol fires can be extinguished with plain water, whereas gasoline floats on water and continues to burn. The EPA has estimated that switching fuels from gasoline to methanol would reduce the incidence of fuel related fires by 90%.