Basically, the capital gains system is taxed at your marginal income tax rate.
First you have to calculate how much profit you have made on the sale. After you have calculated the profit, if the shares were purchased in an individual's name you get to deduct 50% of the profit before adding to your normal income. If there is a loss you cannot deduct from your income tax unless you have other capital gains from other assets.
I have included a list of the steps to the ato website which can help calculate the profit or loss from the sale of your shares.
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