One of the patients is from the NHS Greater Glasgow and Clyde area while the other is from the NHS Lanarkshire area.
The two health boards, along with Health Protection Scotland, said they were investigating two suspected cases of wound botulism.
The investigation is focusing on injecting heroin users.
Dr Gillian Penrice, NHS Greater Glasgow and Clyde consultant in public heath medicine, said: "I urge all drug injecting heroin users to be extremely alert.
"They should seek urgent medical attention from accident and emergency if they experience any early symptoms such as blurred or double vision, difficulty in swallowing and speaking and/or inflammation at the injection site.
"It is important for injecting drug users to engage with the wide range of services we offer designed to help them tackle their addictions. However for those who continue to inject, it is extremely important that they seek urgent medical help if they show these early symptoms."
She added: "Heroin users should avoid injecting heroin into their muscles. Injecting heroin into a vein or smoking can reduce the risk of botulism, although not using heroin at all is by far the best course of action."
Two injecting drug users are being treated in hospital for suspected botulism, it has been confirmed.